Another plot could be that an enemy targets Mount Myoboku to disrupt the balance of chakra in the ninja world. Naruto, along with the toads, has to defend the mountain. He could use the environment of the mountain to his advantage, like using the natural chakra sources there in new and creative ways to fend off the invaders.
One idea could be Naruto discovers a hidden technique in Mount Myoboku that only he can master because of his unique bond with the toads. This technique could give him an edge in a major battle.
Obviously Naruto is one of the most important. He has a strong connection to Mount Myoboku. The Great Toad Sage is also crucial as he often imparts wisdom and prophecies. Gamabunta, Naruto's big toad summon, is important too. He has been with Naruto in many battles and is a powerful ally.
A plot idea could be that Naruto discovers a new, ancient form of chakra that has been lost for centuries. He then has to train to master this chakra while also dealing with the political implications within the Hidden Leaf Village. Some elders might be against him exploring this new power for fear of the unknown, but Naruto, being Naruto, is determined to master it for the good of the village.
One idea could be that the events of 9/11 somehow influence the Hidden Leaf Village. For example, they might tighten security and Naruto could be part of a new team in charge of protecting the village from potential outside threats inspired by the real - world event. Another plot could involve characters from Naruto trying to understand the concept of such a large - scale tragedy and how they can prevent similar things in their own world.
One idea could be that Neji discovers a new hidden power within Naruto that he helps Naruto master. This could lead to them having to face a new, powerful enemy together.
One interesting plot idea could be a time - travel story. For example, Naruto is sent back in time to the era of the First Hokage. He could use his knowledge of future jutsu and events to change things for the better in the past. Another idea is a story where Naruto discovers a hidden clan within Konoha that has a unique and powerful Kekkei Genkai. He then has to help this clan gain acceptance in the village. A third idea might be a story where Naruto is turned into a different creature, like a cat or a fox, and has to find a way to turn back while still dealing with the normal threats to the village.
One interesting storyline could be about Naruto characters being transported into the Mount and Blade world and having to adapt to its combat and political systems. For example, Naruto might use his shadow clone jutsu in battles against the bandits in the Mount and Blade setting.
A great plot could involve the female Naruto being sent on a diplomatic mission to another village. There, she discovers a conspiracy against the Hidden Leaf Village and has to use her wits and ninja skills to expose it and prevent a war. Along the way, she also forms unexpected friendships with some of the villagers from the other village, which helps her in her mission.
A really interesting plot could be a tournament in which both Naruto characters and Pokegirls participate. They have to fight against each other using their respective skills. It would be a test of strategy and power, and also a great opportunity for character development as they learn from one another's fighting styles.
One idea could be that Naruto somehow gets transported to the world where Tiamat exists. He has to use his ninja skills to survive in a completely different and magical realm. Maybe he teams up with local heroes to face a threat that Tiamat also has an interest in.
One idea could be a crossover where Naruto's world is invaded by spirits and Tohka comes to help. Naruto could be intrigued by Tohka's powers and they team up to fight the new threat.